title: Generation of highly proliferative rejuvenated cytotoxic T cell clones through pluripotency reprogramming for adoptive immunotherapy

status: Public on Apr 27 2021

city: Kyoto

first: Akira

last: Watanabe

state: Kyoto

address: Rm504, Miyako Bldg, 233, Isa-cho, kamigyo-ku

institute: CyberomiX Inc

summary: Adoptive immunotherapy has emerged as a powerful approach to cure cancer and chronic infections. Currently, the generation of a massive number of T cells that provide long-lasting immunity is challenged by exhaustion and differentiation-associated senescence, which inevitably arise during in vitro cloning and expansion. To circumvent these problems, several studies have proposed an induced pluripotent stem cell (iPSC)-mediated rejuvenation strategy to revitalize the exhausted/senescent T-cell clones. Because iPSC-derived cytotoxic T lymphocytes (iPSC-CTLs) generated via commonly used monolayer systems have unfavorable innate-like features such as aberrant natural killer (NK) activity and limited replication potential, we modified the redifferentiation culture to generate CD8ab+CD5+CCR7+CD45RA+CD56- adaptive iPSC-CTLs. The modified iPSC-CTLs exhibited early memory phenotype, including high replicative capacity and the ability to give rise to potent effector cells. In expansion culture with an optimized cytokine cocktail, iPSC-CTLs proliferated more than 10^15-fold in a feeder-free condition. Our redifferentiation and expansion package of early memory iPSC-CTLs could supply memory and effector T cells for both autologous and allogeneic immunotherapies.

overall_design: To examine expression of T cell-related genes in iPSC-CTLs, RNA-sequencing were conducted.

first: Yohei

last: Kawai

first: Shin

last: Kaneko


title: RNA-seq analysis of the gene expression profile regulated by Gadd45g in mouse ESCs

status: Public on Apr 22 2021

city: Hefei

first: shoudong

last: ye

address: No 111, Jiu Long Road

department: Cell Biology

country: China

institute: Anhui University

type: Expression profiling by high throughput sequencing

summary: Purpose: The goals of this study is to analyze the gene expession pattern in mouse embryonic stem cells (ESCs) ovexpressed flag or mouse flag tagged gadd45g

overall_design: 46C mouse ESCs overexpressed flag or flag tagged gadd45g and  cultured in serum-containing medium supplemented LIF were collected by using Trizol. These samples were sent to BGI (Shenzhen, China) company to do deep sequencing by using MGI2000.

first: Shoudong

last: Ye


status: Public on Apr 21 2021

city: Xining

first: Juan

last: An

state: Please Select

address: No.251 of Ningzhang Road

institute: Qinghai University

summary:
Total RNA was extracted from AGS cells treated with or without podofilox using TRIzol® reagent (Invitrogen; Thermo Fisher Scientific, Inc.), according to the manufacturer’s protocol. The quality and quantity of the RNA were determined using NanoDrop 2000
PrimeView Human Gene Expression Array was used to profile gene expression.

overall_design: The expression of mRNA after treatment by Podofilox, 8 samples


title: T-bet-Eomes [ChIP-Seq]

status: Public on May 10 2021

city: Lyon

first: Thierry

last: Walzer

address: 21 avenue tony garnier

country: France

institute: CIRI, centre international de recherche en infectiologie

type: Genome binding/occupancy profiling by high throughput sequencing

summary: This project aims at understanding the role of T-bet and Eomes in the differentiation of Natural Killer (NK) cells. NK cells are innate cytotoxic lymphocytes that play an important role in the early control of viral infections and in immune surveillance of cancers. T-bet and Eomes are related T-box factors that are co-expressed by NK cells and are supposed to bind to similar DNA motifs. Their role in NK cell differentiation are not very well understood, in part because their direct target genes are unknown. This study is designed to identify T-bet and Eomes target genes in NK cells. It is based on two complementary mouse strains that we generated in the lab that express tagged (HA) forms of T-bet or Eomes. The tag sequences were inserted in the C-terminus region of both factors, by homomogous recombination in ES cells, allowing endogenous regulation of T-bet and Eomes.

overall_design: Two Chip replicates were performed for each genotype (Eomes-HAV5,  T-bet-HAV5, and control ie C57BL/6). Fpr each Chip 10 millions spleen NK  cells were used as starting material and the Chip was performed using  anti-HA antibody.


title: Single-cell RNA-seq identification of the cellular molecular characteristics of sporadic bilateral clear cell renal cell carcinoma

status: Public on May 05 2021

city: Nanning

first: Zhenyuan

last: Yu

state: Guangxi

address: Shuangyong road 22

department: Center for Genomic and Personalized Medicine

institute: Guangxi Medical University

summary: Bilateral renal cell carcinoma (RCC) is a rare type of this disease and includes familial bilateral and sporadic bilateral RCCs. Studying the cellular molecular characteristics of sporadic bilateral is important to provide a direct guide for clinical treatment. These cellular molecular characteristics can be expressed at the RNA level, especially at the single-cell RNA level. Single-cell RNA sequencing (scRNA-seq) was performed on bilateral clear cell RCC (ccRCC). A total of 3,575 and 3,568 high-quality single-cell transcriptome data were captured from the left and right tumour tissues, respectively. Gene characteristics were identified by comparing left and right tumours at the scRNA level. This work presented the complex cellular environment of bilateral ccRCC by scRNA-seq. Single-cell transcriptome analysis revealed high similarity in gene expression among most cell types of bilateral RCCs but significant differences in gene expression among different site tumour cells. Additionally, the potential biological function of different tumour cell types was determined by gene ontology (GO) analysis. The transcriptome characteristics of tumour tissues in different locations at the single-cell transcriptome level were revealed through the scRNA-seq of bilateral sporadic ccRCC. This work provides new insights into the diagnosis and treatment of bilateral RCC.

overall_design: Primary kidney samples from 3 patients were used for single cell RNA sequencing by 10X Genomics

first: Wenhao

last: Lu

first: Cheng

last: Su

first: Yufang

last: Lv

first: Yu

first: Bingqian

last: Guo

first: Deyun

last: Liu

first: Haibiao

last: Yan

first: Hua

last: Mi

first: Tianyu

last: Li

first: Qingyun

last: Zhang

first: Jiwen

last: Cheng

first: Zengnan

last: Mo


title: EHF is essential for epidermal and colonic epithelial homeostasis and suppresses Apc-initiated colonic tumorigenesis

city: Heidelberg

first: John

middle: M

last: Mariadason

state: Victoria

address: Austin Health, 145 Studyley Road

department: Gastrointestinal Cancers

country: Australia

institute: Olivia Newton-John Cancer Research Institute

summary: We report the gene expression differences in the colonic epithelium of control and Ehf knockout mice assessed by RNA-seq analysis.

overall_design: We performed RNA-seq analysis of colonic epithelial cells isolated from 6-week-old Ehf WT and Ehf intestinal knockout (IKO) mice. To account for possible transcriptional changes induced by tamoxifen, Villin CreERT2 mice treated with tamoxifen (Villin CreERT2-TMX) were also analyzed as a further control

first: Camilla

last: Reehorst


title: Decoding dynamic epigenetic landscapes in human oocytes using single-cell multi-omics sequencing

status: Public on May 07 2021

city: Beijing

first: Fan

state: Beijing

address: 1 Beichen West Road, Chaoyang District

department: The State Key Laboratory of Stem Cell and Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

type: Methylation profiling by high throughput sequencing

summary: Developing female human germ cells undergo genome-wide epigenetic reprogramming, but de novo DNA methylation dynamics and their interplay with chromatin states and transcriptional activation in developing oocytes is poorly understood. Here, we developed a single-cell multi-omics sequencing method, scChaRM-seq, that enables simultaneous profiling of the DNA methylome, transcriptome, and chromatin accessibility in single human oocytes and ovarian somatic cells. We observed a global increase in DNA methylation during human oocyte growth that correlates with chromatin accessibility, whereas increases of DNA methylation at specific features were associated with active transcription. Integrated analyses of multi-omics data from humans and mice revealed species-specific gene expression, and promoter accessi- bility contributes to gene body methylation programs. Alu elements retained low DNA methylation levels and high accessibility in early growing oocytes and were located near developmental genes in humans and mice. Together, these findings show how scChaRM-seq can provide insight into DNA methylation pattern estab- lishment.

overall_design: 953 single human oocytes and somatic cells were performed by scChaRM-seq. Only 899 single cells that passed through the quality control were uploaded.

first: Chan

last: Gu

first: Rui


title: Comparison of DEG between memantine-, vehicle-treated and naive Shank2 wild-type and knock-out mice

status: Public on Apr 20 2021

city: Daejeon

first: Eunjoon

last: Kim

address: Kuseong-dong

department: Center for Synaptic Brain Dysfunctions/Department of Biological Sciences

country: South Korea

institute: IBS/KAIST

summary:
Autism spectrum disorders (ASDs) are thought to involve diverse neurodevelopmental dysregulations that lead to visible symptoms at early stages of life. Many ASD-related mechanisms suggested by animal studies are supported by demonstrated improvement in autistic-like phenotypes in adult animals following experimental reversal of dysregulated mechanisms. However, whether such mechanisms also act at earlier stages to play important roles in the development of autistic-like phenotypes is unclear. Here, we show that early correction of a dysregulated mechanism in young mice prevents manifestation of autistic-like phenotypes in adult mice. Shank2–/– mice, known to display N-methyl-D-aspartate receptor (NMDAR) hypofunction and autistic-like behaviors at post-weaning stages after postnatal day 21 (P21), show the opposite synaptic phenotype—NMDAR hyperfunction—at an earlier pre-weaning stage (~P14). Moreover, this NMDAR hyperfunction at P14 is rapidly shifted to NMDAR hypofunction after weaning (~P24). Chronic suppression of the early NMDAR hyperfunction in Shank2–/– mice by the NMDAR antagonist memantine before weaning (P7–21) prevents the NMDAR hypofunction and autistic-like behaviors from manifesting at later stages (~P28 and P56). In addition, early memantine treatment of Shank2–/– mice substantially alters transcription of numerous genes, driving gene expression patterns in a direction largely opposite that observed in drug-untreated Shank2–/– mice, which, interestingly, mimic those observed in autistic individuals. These results suggest that early NMDAR hyperfunction in Shank2–/– mice leads to late NMDAR hypofunction and autistic-like behaviors, and that early correction of NMDAR function has the long-lasting effect of preventing autistic-like phenotypes from developing at later stages.

This SuperSeries is composed of the SubSeries listed below.

overall_design:
Whole brain transcriptome of 3 naïve P14, naïve P25, early memantine treated WT and Shank2 knock-out mutant mice in both sex.

Refer to individual Series


title: Transcriptome analyses of aggregating Lactiplantibacillus plantarum

city: Zürich

first: Marc

last: Stevens

address: Winterthurerstrasse 272

department: Vetsuisse

country: Switzerland

institute: University of Zurich

summary: The transcriptome of L. plantarum strains that aggregate was compared with non-aggregating strains

overall_design: 2 aggregating strain with 2 and 3 samples. 2 non-aggregating strains with 3 samples each.

first: Julia

last: Isenring

first: Annelies

last: Geirnaert

first: Christophe

last: Lacroix


title: Transcriptomic analysis of THAP1 mediated oligodendrocyte development

status: Public on Apr 24 2021

city: Ann Arbor

first: Dhananjay

last: Yellajoshyula

state: MI

address: 5378, BSRB, 109, Zina Pitcher Place

department: Neurology

country: USA

institute: University of Michigan

summary: We demonstrated previously that THAP1 plays a cell-autonomous role in regulating myelination during early postnatal CNS development (Yellajoshyula et al., Dev Cell, 42, 52-67, 2017). To begin to examine the mechanisms responsible for this role, we performed RNAseq at multiple time points on cultured control (Thap1+/+) and Thap1 null (derived from Thap1flx/-; Olig2-Cre+) OPC under differentiating conditions.

overall_design: RNA-Seq analysis for 3 individual clones of Control and Thap1 null OPC differentiated  for days 0, 2 & 4.

first: Xylena

last: Reed

first: Jinhui

last: Ding

first: Mark

middle: R

last: Cookson

first: William

middle: T

last: Dauer


title: MarR type regulator PA3458 is involved in osmoadaptation control in Pseudomonas aeruginosa (RNA-seq)

status: Public on Apr 12 2021

city: Warszawa

first: Adam

last: Kawałek

address: Pawinskiego 5A

department: Department of Microbial Biochemistry

country: Poland

institute: Institute of Biochemistry and Biophysics, PAS

summary: Pseudomonas aeruginosa is a common bacterium, but also a facultative human pathogen, especially fatal for immunocompromised patients. It is dangerous due to its high adaptability and intrinsic antibiotic resistance mechanisms making treatment of P. aeruginosa infections particularly difficult. Sophisticated, complex, multilevel regulatory systems engaging huge repertoire of transcriptional regulators (TRs) are the main factors that direct cellular processes to keep cellular homeostasis and adapt to changeable conditions. The PA3458 gene encodes a putative MarR-type TR. Most representatives of MarR family are described as repressors involved in response to various environmental signals and control of different processes e.g. adhesion, virulence, antibiotic resistance. Transcriptional profiling of P. aeruginosa PAO1161 overexpressing PA3458 showed changes in mRNA level of 133 genes, among them 100 was down-regulated, pointing out the role of PA3458 as a repressor. ChIP-seq analysis identified multiple PA3458 binding sites in P. aeruginosa genome suggesting its role as a global regulator. The preferred sequence motif recognised by PA3458 was identified. Many genes involved in stress response are under control of PA3458. The PA3459-PA3461 operon, divergent to PA3458 gene is regulated by PA3458. It encodes: asparagine synthase, GNAT-family acetyltransferase and glutamyl aminopeptidase, respectively engaged in the production of potent osmoprotectant an N-acetylglutaminylglutamine amide (NAGGN). Overall, the PA3458 is engaged in osmoadaptation control in P. aeruginosa.

overall_design: Pseudomonas aeruginosa PAO1161 (leu-, r-, RifR) derivative of PAO1 was used in the experiment (Kawalek et al., 2020; BMC Genomics, 21:14). To determine the impact of an increased PA3458 level on the transcriptome, the RNA-seq analysis was performed on RNA isolated from Pseudomonas aeruginosa PAO1161/pKKB2.11 carrying araC araBADp-PA3458, hereafter referred to as PA3458, as well as from P. aeruginosa PAO1161 carrying pKGB8 (araC araBADp) - empty vector control (hereafter called EV). Cells were grown under selection in L broth with 0.02% arabinose. RNA was isolated from exponentially growing cultures (OD600 0.5). Three independent biological replicates of total RNA were isolated for each strain.

first: Karolina

last: Kotecka

last: Kawalek

first: Aneta

middle: A

last: Bartosik


title: Modeling acute myocardial infarction in vitro using mature and ventricular hESC-derived cardiomyocytes by FGF4 and ascorbic acid treatment

status: Public on Apr 11 2021

city: Seoul

first: Seung-Cheol

last: Choi

address: Anamdong 5-Ga

department: Cardiology

institute: College of Medicine, Korea University

summary: hPSC-CMs resemble immature embryonic or fetal CMs rather than mature adult CMs, and have limitations in disease modeling and pharmacological studies. Therefore, hPSCs-derived mature and ventricular CMs are required for more accurate in vitro modeling of adult-onset cardiac disease and drug discovery. FGF4+AA-treated hESC-CMs robustly released acute myocardial infarction (AMI) biomarkers (cTnI, CK-MB, and myoglobin) into culture medium in response to hypoxic injury. Hypoxia-responsive genes related to cellular responses to glycolytic processes, oxygen levels, HIF-1 signaling, apoptotic processes, and regulation of cell death including potential cardiac biomarkers proved in clinical studies in the diagnosis and prognosis of coronary artery diseases were induced in FGF4+AA-treated hESC-CMs in response to hypoxia based on transcriptome analyses.

overall_design: RNA profiles of normoxia- and hypoxia-treated BG01 hESC-CMs for 24 hr after treatment with FGF4+AA between days 5 and 15 of differentiation

first: Ha-Rim

last: Seo

first: Long-Hui

last: Cui

first: Myeong-Hwa

last: Song

first: Ji-Min

last: Noh

first: Kyung-Seob

first: Ji-Hyung

first: Jong-Ho

first: Chi-Yeon

last: Park

first: Hyung

middle: J

last: Joo

first: Soon

last: Hong

first: Tae

middle: H

last: Ko

first: Jong-Il

first: Hyo

first: Jong-Hoon

first: Se-Hwan

last: Paek

first: Ji-Na

first: Dong-Hyung

first: Yongjun

last: Jang

first: Yongdoo

first: Do-Sun

last: Lim


title: A multi-omics angle sheds light on the molecular mechanisms underlying desiccation tolerance in Craterostigma plantagineum

status: Public on Apr 30 2021

city: Belvaux

first: Sylvain

last: Legay

address: 41, rue du Brill

department: ERIN department

country: Luxembourg

institute: Luxembourg Institute of Science and Technology

summary: The resurrection plant Craterostigma plantagineum possesses an extraordinary capacity to survive long-term desiccation. To enhance our understanding of this phenomenon, complementary transcriptome, soluble proteome and primary metabolome analyses were carried out on plant leaves collected from different physiological stages during a dehydration and rehydration cycle. A total of 7348 contigs, 611 proteins and 46 metabolites were differentially regulated across stages. Dynamic changes in transcript, protein and metabolite levels revealed a unique signature characterizing each stage. An overall low correlation between transcript and protein abundance suggests a prominent role for post-transcriptional modification in metabolic reprogramming to prepare plants to desiccation and recovery upon rehydration. The integrative analysis of three -omics datasets was performed with an emphasis on photosynthesis, photorespiration, energy metabolism and amino acid metabolism. The results revealed a set of fine regulations/changes that modulate primary metabolism to confer plasticity to metabolic pathways, thus optimizing plant performance under stress. For example, maintenance of cyclic electron flow and photorespiration and switch from C3 to Crassulacean acid metabolism (CAM) photosynthesis may contribute to partially sustain photosynthesis and minimize oxidative damage during dehydration.  transcripts with a delayed translation, ATP-independent bypasses, alternative respiratory pathway and 4-aminobutyric acid (GABA) shunt may play a role in energy management, altogether conferring bioenergetic advantages to  meet energy demands for survival during desiccation. This knowledge provides a high-resolution map of the changes occurring in the primary metabolism during dehydration and rehydration and enriches the current understanding of the molecular mechanisms underpinning plant desiccation tolerance. The datasets here provided will ultimately inspire biotechnological strategies for drought tolerance improvement in crops.

overall_design: Multi-Omics analysis of the time-course kinetic of the dehydration and rehydration of the Craterostigma plantagineum resurection plant

first: Xuan

last: Xu

first: Kjell

last: sergeant

first: Simone

last: Zorzan

first: Céline

middle: C

last: Leclrecq

first: Sophie

last: Charton

first: Valentino

last: Giarola

first: Jenny

last: Renaut

first: Jean-Francois

last: Hausman

first: Dorothea

last: Bartels

first: Gea

last: Guerriero


title: The SUN1-SPDYA interaction plays an essential role in meiosis prophase I

status: Public on Apr 08 2021

city: Shanghai

first: Qian

last: Bian

state: Shanghai

address: Pudong New District, Jinzun Rd, No.115

department: Ninth People’s Hospital

institute: Shanghai Jiao Tong University School of Medicine

summary: Chromosomes pair and synapse with their homologous partners to segregate correctly at meiosis I. Association of telomeres with the LINC (Linker of Nucleoskeleton and Cytoskeleton) complex enables telomere-led chromosome movements and telomere bouquet formation, facilitating precise pairwise alignment of homologs. Here, we identify a direct interaction between SUN1 and Speedy A (SPDYA) and determine the crystal structure of human SUN1-SPDYA-CDK2 ternary complex. Analysis of meiosis prophase I process in SPDYA-binding-deficient SUN1 mutant mice reveals that the SUN1-SPDYA interaction is required for the telomere-LINC complex connection and the assembly of a ring-shaped telomere supramolecular architecture at the nuclear envelope, which is critical for efficient homologous pairing and synapsis. Overall, our results provide structural insights into meiotic telomere structure that is essential for meiotic prophase progression.

overall_design: Hi-C experiment to Sun1 W151R pachytene-like spermatocytes

first: Wu

last: Zuo


title: Identification of significantly differential expression of long noncoding RNAs and pathways in hepatic fibrosis rat liver issues

status: Public on Apr 23 2021

city: 成都

first: 熊

last: 肖

address: 四川省成都市文江区万春镇

institute: 成都中医药大学附属第五人民医院

type: Non-coding RNA profiling by high throughput sequencing

summary: Objective: To identify the long noncoding (lncRNA) and its potential roles in hepatic fibrosis rat liver issues induced by CCl4. Methods: LncRNAs and genes were analyzed in fibrosis rat liver issues by RNA sequencing and verified by quantitative reverse transcription polymerase chain reaction (qRT-PCR). Differential expressed lncRNAs and genes were subjected to bioinformatics analysis and involved to construct co-expression network.

overall_design: LncRNAs and genes were analyzed in 3 fibrosis rat liver issues and 3 control rat liver issues by RNA sequencing.

first: Yan

last: Wang

first: Xiong

last: Xiao


title: Comparison of transcriptomic profiles in natural populations of rodents (house mouse and black rat) along invasion routes in Senegal

status: Public on Apr 09 2021

city: Montferrier-sur-Lez

first: Maxime

last: Galan

address: 755 avenue du campus Agropolis

institute: INRA

summary: We compared gene expression proﬁles between anciently and recently established populations of two major invading species, the black rat Rattus rattus and the house mouse Mus musculus musculus, in Senegal. Transcriptome analyses revealed respectively 364 and 83 differentially expressed genes along the mouse and rat invasion routes. Among them, 10 and 15% were annotated with functions related to immunity. All immune-related genes detected along the mouse invasion route were over-expressed at the invasion front. Genes of the complement activation pathway were over-represented. Results were less straightforward when considering the black rat. No particular immune pathway was over-represented. In conclusion, we revealed changes in transcriptomic profiles along invasion routes. Patterns differed between invaders. They could potentially be driven by increased infection risks at invasion front for the house mouse and trade-offs between immune responses for the black rat. Our results provide a first step in identifying the immune ecoevolutionary processes potentially involved in invasion success.

sample_organism:
Mus musculus
Rattus rattus

platform_organism:
Mus musculus
Rattus rattus

overall_design: Comparison of transcriptomic profiles based on pools of mRNA (extracted from spleen) for rodents sampled in anciently and recently invaded localities. We considered 2 replicates per locality and 4 localities per invasion status 'ancient vs recent establishment of populations'

first: Nathalie

last: Charbonnel

first: Caroline

last: Tatard

first: Anne

last: Loiseau

first: Christophe

last: Diagne

first: Orianne

last: Tournayre

first: Hughes

last: Parinello

first: Stephanie

last: Rialle

first: Dany

last: Severac

first: Carine

last: Brouat


title: Next generation sequencing transcriptome analysis of colonic epithelial cells from bone marrow transplant recipient mice

status: Public on Apr 01 2021

first: Keisuke

last: Seike

address: 1500 E. Medical Center Drive

department: Internal Medicine

summary: Alloimmune T cell mediated gastrointestinal graft-versus-host disease (GI-GVHD) occur after bone marrow translantation (BMT). GI-GVHD cause significant morbidity and mortality. Immunosuppression therapies have shown good results with adverse effects, but are still incomplete. The biology of GVHD are often understood from the immune cell perspectve, but the pathogenesis and severity from host IEC traget cell perspective remain undefined.  We used next generation sequencing transcriptome to detail the gene expression of colonic epithelial cells underlying the profile changes between the syngeneic recipient and allogeneic recipient.

overall_design: C57BL/B6 mice used as recipients. Donor mice were C57BL/B6 for syngeneic group and BALB/c for allogeneic group. Recipient mice were received 1000cGy TBI on day -1 and were injected 2 million CD90.2+ T cells and 5 million bone marrow cells on day 0. Colonic epithelial cells were isolated from recipient mice on BMT day7 and processed for RNA isolation.  Naive C57BL/B6 mice mached with age and sex were seclected .

first: Michael

last: Brooks

first: Hideaki

last: Fujiwara

first: Reddy

last: Pavan


title: Expression data from co- and mono-cultured human brain microvascular endothelial cells and human brain vascular pericytes treated with and without estradiol

status: Public on Apr 19 2021

city: Schlieren

first: Lisa

middle: Maria

last: Kurmann

address: Wagistrasse 14

department: Reproductive endocrinology

institute: University Hospital Zurich

summary:
For the formation of the blood-brain barrier not only endothelial cells alone, but also their interaction with surrounding cell types, like pericytes, plays an important role, and co-culture of the two cell types increases barrier function in vitro. Furthermore, observed sex differences with regard to several cardiovascular as well as neurodegenerative disorders have led to the hypothesis that the female sex hormone estrogen might protect from endothelial barrier break-down.
Microarray analysis was performed to determine the effect of co-culture on the gene expression profiles of pericytes and endothelial cells. Additionally, cells were treated with and without estradiol in order to determine possible effects of the sex hormone on the two cell types in mono- and co-cultures.

overall_design: We cultured human brain pericytes and the human brain microvascular endothelial cell line (hCMEC/D3) alone and together on the opposite sides of a porous transwell insert, allowing the formation of direct contacts between the two cell-types as well as the exchange of secreted factors between the apical and basolateral chamber. Cells were cultured for a total of 7 days, and the last 48h of culture estradiol treatment was added, before cells were lysed for RNA isolation.

first: Michal

last: Okoniewski

first: Raghvendra

middle: K

last: Dubey


title: A global transcriptome analysis of human keratinocyte cell line HaCaT overexpressing the miR-21-3p.

status: Public on Apr 02 2021

city: Orléans

first: Chantal

last: Pichon

address: Rue Charles Sadron

institute: Centre de Biophysique Moléculaire, CNRS-UPR4301

summary: Psoriasis is a chronic inflammatory skin disease that is mediated by a complex crosstalk between immune cells and keratinocytes (KCs). Emerging studies showed a specific psoriatic microRNAs signature where miR-21 is one of the most upregulated miRNAs. In this study, we focused our investigations on the passenger miR-21-3p strand that is poorly studied in skin and in psoriasis pathogenesis. Here, we transfected the HaCaT cells with synthetic oligoncucleotides form of miR-21-3p and evaluated the impact of the over-expression of this miRNA in these call by RNA-seq analysis. We identified a network of differentially expressed genes involved in abnormal proliferation control and immune regulatory genes implicated in the molecular pathogenesis of psoriasis in response to miR-21-3p overexpression in KCs. These results were confirmed by functional assays that validate the proliferative potential of miR-21-3p. All these findings highlight the importance of miR-21-3p, an underestimated miRNA, in psoriasis and provide novel molecular targets for therapeutic purposes.

overall_design: HaCaT cells were transfected with negative control or miR-21-3p mimics before extracting the total RNA fraction of cells 48h later and enriching polyA RNA. The samples are composed of 3 biological replicates from HaCaT cells transfected with a synthetic negative control miRNA (mimic CTL) as well as 3 biological replicates from HaCaT cells transfected with synthetic miR-21-3p mimics (mimic).

first: Florence

last: Abdallah

first: Elodie

last: Henriet

first: Amandine

last: Suet

first: Ali

last: Arar

first: Rudy

last: Clemençon

first: Jean-Marc

last: Malinge

first: Gaël

last: Lecellier

first: Patrick

last: Baril


title: Hoxa10 mediates positional memory to govern stem cell function in adult skeletal muscle

status: Public on Apr 17 2021

city: Kumamoto

first: Yusuke

last: Ono

state: Kumamoto

address: 2-2-1 Honjo

department: Institute of Molecular Embryology and Genetics

country: Japan

institute: Kumamoto University

summary: Muscle stem cells (satellite cells) are distributed throughout the body and have heterogeneous properties among muscles. However, functional topographical genes in satellite cells of adult muscle remain unidentified. Here, we show that expression of Homeobox-A (Hox-A) cluster genes accompanied with DNA hypermethylation of the Hox-A locus was robustly maintained in both somite-derived muscles and their associated satellite cells in adult mice, which recapitulates their embryonic origin. Somite-derived satellite cells were clearly separated from cells derived from cranial mesoderm in Hoxa10 expression. Hoxa10 inactivation led to genomic instability and mitotic catastrophe in somite-derived satellite cells in mice and human. Satellite cell–specific Hoxa10 ablation in mice resulted in a decline in the regenerative ability of somite-derived muscles, which were unobserved in cranial mesoderm–derived muscles. Thus, our results show that Hox gene expression profiles instill the embryonic history in satellite cells as positional memory, potentially modulating region-specific pathophysiology in adult muscles.

overall_design: Skeletal muscles were harvested from male, 12-week-old mice (C57BL/6J).

first: Kiyoshi

last: Yoshioka


title: Transcriptomic profiling of cortical bone from hindlimb unloaded mice

status: Public on Mar 23 2021

city: Boston

first: Frank

last: Ko

address: 330 Brooline Ave RN120

institute: Beth Israel Deaconess Medical Center

summary: The goal of this study was to perform RNA-sequencing of cortical bone isolated from 11-week-old female hindlimb unloaded and control mice.  Mice were subjected to hindlimb unloading for 7 days, followed by RNA isolation of cortical bone.  Cortical transcriptomic profiles were assessed with RNAseq.

overall_design: 11-week-old female hindlimb unloaded vs control mice (n=8/group)

first: Jordan

last: Spatz

first: Ugur

last: Ayturk

first: Matthew

last: Warman

first: Mary

last: Bouxsein


title: Ischemia Reperfusion of Lung Transplant Setting Differentially Regulates Transcriptomic Profiles between Human Lung Endothelial and Epithelial Cells

city: Toronto

first: Aaron

last: Wong

state: Ontario

address: 101 College Street

department: TGHRI

country: Canada

institute: University Health Network

summary: Our understanding on mechanisms of ischemia-reperfusion induced lung injury during lung preservation and transplantation is based on clinical observations and animal studies. Herein, we used cell and systems biology approaches to explore these mechanisms at transcriptomics levels, especially by focusing on the differences between human lung endothelial and epithelial cells, which are crucial for maintaining essential lung structure and function. Human pulmonary microvascular endothelial cells and human lung epithelial cells were cultured to confluent, subjected to different cold ischemic time (CIT) to mimic static cold storage with preservation solution, and then subjected to warm reperfusion with serum containing culture medium to similar lung transplantation. Cell morphology, viability and transcriptomic profiles were studied. Ischemia-reperfusion induced a CIT time-dependent cell death, which was associated with dramatic changes in gene expression. Under normal control conditions, endothelial cells showed gene clusters enriched in vascular process and inflammation, while epithelial cells showed gene clusters enriched in protein biosynthesis and metabolism. CIT 6 h alone or after reperfusion had little effects on these phenotypic characteristics. After CIT 18 h, protein biosynthesis related gene clusters disappeared in epithelial cells; after reperfusion, metabolism-related gene cluster in epithelial cells and multiple gene clusters in the endothelial cells also disappeared. Human pulmonary endothelial and epithelial cells have distinct phenotypic transcriptomic signatures. Severe cellular injury reduces these gene expression signatures in a cell type dependent manner. Therapeutics that preserve these transcriptomic signatures may represent new treatment to prevent acute lung injury during lung transplantation.

overall_design: This study compared gene expression of BEAS2B cells and HPMEC cells cultured in vitro. 5 conditions were simulated for each cell type: untreated (growth media), 6 hours cold ischemia, 18 hours cold ischemia, 6 hours cold ischemia + 2 hours reperfusion, 18 hours cold ischemia + 2 hours reperfusion

first: Gaowa

last: Saren

first: Yunbi

last: Lu

first: Cristina

last: Baciu

first: Wenyong

last: Zhou

first: Ricardo

last: Zamel

first: Sahar

last: Soltanieh

first: Junichi

last: Sugihara

first: Mingyao

last: Liu


title: Comparison between lncRNA-HAL silenced MCF7 cells and control shLuc MCF7 cells

status: Public on Apr 21 2021

city: México

first: Vilma

middle: Araceli

last: Maldonado

state: Distrito Federal

address: Periferico  4809

department: Investigacion

country: Mexico

institute: INMEGEN

summary: Analysis of differentially expressed genes in MCF7 cancer cells stably silenced with shlncHAL-2 short-hairpin versus control MCF7 cells stably expressing control shLuc short-hairpin.

overall_design: Two groups were analyzed in triplicate or quadruplicate. The first group was MCF7 stably transfected with a vector expressing shlnc-HAL-2 for lncRNA-HAL knock-down and the second group was an MCF7 cell line stably transfected with a vector expressing shLuc control hairpin.

first: Alfredo

last: García

first: Jorge

last: Melendez


title: Identification of Nfia-target genes in mid-gestational NS/PCs

status: Public on Apr 15 2021

city: Fukuoka

first: Jun

last: Takouda

address: 3-1-1, Maidashi

institute: Kyushu University

summary: The purpose of this study is to identify Nfia-target genes, and then clarify how Nifa induces gliogenic potential during brain development.

overall_design: Profiles of Nfia binding sites and  transcriptome of control and Nfia-transduced NS/PCs at 3 days after transduction were obtained by deep sequencing, using Illumina Hiseq 2500.

first: Sayako

last: Katada

first: Taito

last: Matsuda

first: Kinichi

last: Nakashima


title: RNA-seq analysis of human asthma bronchoalveolar lavage (BAL) cells

city: Pittsburgh

first: Anuradha

last: Ray

state: PA

address: 3459 Fifth Ave, MUH 628 NW

department: Medicine/Pulmonary

institute: University of Pittsburgh

summary: Next-generation sequencing of human BAL cells obtained from human patients with differing degrees of asthma in a search for variations in gene expressions.

overall_design: Analysis of gene expression obtained from human BAL cells comparing healthy, mild or severe asthma.

first: Sally

last: Wenzel


title: ChIRC-seq  Reveals Promoter Antisense RNAs and HP1α as Key Regulators of Promoter Pause Release and of Enhancer : Architectural RNA Interactions [ChIRC-seq]

status: Public on Mar 24 2021

city: La Jolla

first: MICHAEL

middle: G

last: ROSENFELD

state: CA

address: 9500 Gilman Drive

institute: HHMI/UCSD

summary: Demonstration of a massive lncRNA RNA transcriptional program in the mammalian genome has engendered lively discussions about their biological roles, particularly the promoter antisense (PAS) transcripts of coding gene transcription units and abundant species localized to specific subnuclear structures with phase separation properties. Here, we report development of an alternative assay to quantitatively detect RNA distribution in the genome, referred to as ChIRC-seq (Chromatin Isolation by RNA-Cas13a Complex Capture by Cas13a), which has revealed that promoter antisense RNAs (PAS-RNAs) serve as a key gatekeeper of a broad transcriptional pause release program, based on decommissioning the 7SK snRNA-dependent inhibitory P-TEFb complex. Induction of PAS-RNA by liganded estrogen receptor ERα (ESR1) releases the basal recruitment of HP1α and KAP1 on target gene promoters, without the spreading characteristic of extended heterochromatic regions, based on PAS-dependent recruitment of H3K9me3 demethylases. Unexpectedly, ERα-bound MegaTrans enhancer activation with features of phase separation events proved to require recruitment of phosphorylated KAP1 to be activated, with its transfer to the cognate promoters licensing estrogen-induced pause release and target gene activation.  The ChIRC13a-seq method has proved effective for identification of the cognate promoter for activated enhancers and has revealed that the lncRNAs NEAT1/MALAT1 in phase-separated subnuclear structures interact with robust estrogen-activated MegaTrans TFF1e1 enhancer and other active enhancers, linking acute activation of a subset of enhancers to interactions with specific phase-separated subnuclear architectural structures.

overall_design: The changes in the gene expression profiles were investigated by ChIP-seq, PRO-seq, and ChIRC-seq.

first: Fan

last: Yang

first: Bogdan

last: Tanasa

first: Rudi

last: Micheletti

first: Kenneth

last: Ohgi

first: Michael

last: Rosenfeld


title: Radiation-induced gliomas represent H3-/IDH-wild type pediatric gliomas with recurrent PDGFRA amplification and loss of CDKN2A/B.

city: Heidelberg

first: Christopher

last: Previti

state: Baden-Wuerttemberg

address: Im Neuenheimer Feld 280

department: Omics IT and Data Management Core Facility (W610)

country: Germany

institute: DKFZ (German Cancer Research Center)

summary: Long-term complications such as radiation-induced second malignancies occur in a subset of patients following radiation-therapy, particularly relevant in pediatric patients due to the long follow-up period in case of survival. Radiation-induced gliomas (RIGs) have been reported in patients after treatment with cranial irradiation for various primary malignancies such as acute lymphoblastic leukemia (ALL) and medulloblastoma (MB). We perform comprehensive (epi-) genetic and expression profiling of RIGs arising after cranial irradiation for MB (n=23) and ALL (n=9). Our study reveals a unifying molecular signature for the majority of RIGs, with recurrent PDGFRA amplification and loss of CDKN2A/B and an absence of somatic hotspot mutations in genes encoding histone 3 variants or IDH1/2, uncovering diagnostic markers and potentially actionable targets.

overall_design: We perform expression profiling of RIGs arising after cranial irradiation for MB and ALL.

first: D

last: Jones

first: S

last: Pfister


title: Gene expression profile of cancerous and non-cancerous renal tissues

status: Public on Mar 14 2021

city: Vilnius

first: Raimonda

last: Kubiliūtė

state: Saulėtekis

address: Sauletekio al., 7

department: Life Sciences Center

country: Lithuania

institute: Vilnius University

summary: Clear cell renal cell carcinoma (ccRCC), is the most common subtype of kidney tumors and characterised by the highest mortality rates among the genitourinary cancers. The currently used models for predicting patient outcome, are based on clinicopathological features only, however patients with similar measures can still have divergent outcomes. This study aimed at identification of novel prognostic DNA methylation biomarkers to aid in predicting patient survival. As DNA methylation in the most cases is related to alteration of gene expression,  firstly, SurePrint G3 Human GE 8×60K Microarrays were used for gene expression profiling in 4 ccRCC tissues and paired non-cancerous renal tissue (NRT) samples. The DNA methylation status of four down-regulated genes were evaluated in 123 ccRCC and 45 NRT samples by means of methylation specific PCR (MSP). Microarray-based transcriptome comparison of 4 ccRCC and 4 NRT samples identified 3942 genes, that were significantly deregulated (P < 0.050) with absolute fold change (FC) value of ≥2. A half of these genes (N = 1958) were down-regulated and four of such genes with moderate-to-high alteration were selected for the further DNA methylation analysis. DNA hypermethylation of all selected genes were cancer specific (P<0.050) with the frequency in tumour tissues ranging from 18 to 42%. The methylated status of at lest one gene showed significant associations with larger tumor size, higher Fuhrman and WHO/ISUP grades as well as the presence of tumor intravascular invasion and necrosis. Moreover, the methylated status of the panel of tree genes was highly predictive for poorer overall survival and  outperformed the prognostic value of tumor stage and tumor necrosis. In conclusion, the three-gene DNA methylation biomarker panel predicts outcome of patients with ccRCC and might be used to improve current prognostic models.

overall_design: Gene expression profile was analyzed in 4 ccRCC cases and paired NRT samples (as a control). No biological replicates were performed.

last: Kubiliute

first: Sonata

last: Jarmalaite


title: CloneSeq: A Highly Sensitive Single-cell Analysis Platform for Comprehensive Characterization of Cells from 3D Culture

city: Jerusalem

first: Xue

last: Sun

address: Hebrew University, Givat Ram campus

department: Biochemistry department

country: Israel

institute: The Hebrew University of Jerusalem

summary: Single-cell assays have revealed the scope and importance of heterogeneity in many biological systems. However, low sensitivity makes it difficult to delineate biological variation from noise, and as a result, the capacity of such assays to identify cellular state differences that arise from genes expressed at low-to-mid abundance is highly limited. To overcome this limitation, we developed CloneSeq, a microfluidics-based technology for 3D-culturing and RNA sequencing (RNA-seq) of small clones. CloneSeq shows that unlike random cell groups, clonal cancer cells originating from a single cell share similar transcriptional profiles. CloneSeq also dramatically improves sensitivity compared to standard single-cell RNA-seq. CloneSeq analysis of non-small cell adenocarcinoma cells revealed the presence of novel cancer-specific subpopulations, including cancer stem-like cells (CSLCs). Based on expression signatures, we identify CSLCs in highly proliferative clones, suggesting that our 3D culturing system promotes stemness. Supporting this, ESCs grown within the 3D hydrogel spheres retained their pluripotent state in the absence of pluripotent media. Moreover, reprogramming efficiency of mouse embryonic fibroblasts within the 3D spheres was significantly improved relative to that of cells grown on gelatin-coated plates. Our results highlight CloneSeq as an extremely useful tool for capturing lowly-expressed genes within clones, and for identifying rare cell populations such as stem-like and cancer-initiating cells.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
Bulk RNA-seq of human (PC9) cells that were genomically barcoded and expanded inside hydrogel spheres (3D) and in a standard tissue culture (2D); and a bulk RNA-seq analysis of mouse embryonic stem (ES) cells grown in hydrogel spheres (3D) and on gelatin (2D) without supporting factors (2i/LIF) for 4 days, with 2 replicates for each experiment.
CloneSeq analysis of  human (PC9) cells with two replicates; a single cell RNA-seq (inDrop) analysis of human (PC9); a single cell RNA-seq (inDrop) analysis of human (PC9) cells that were genomically barcoded and expanded inside hydrogel spheres (3D) with three replicates; and a bulk RNA-seq analysis of mouse embryonic stem (ES) cells grown in hydrogel spheres (3D) with doxycline, with and without supporting factors (2i/LIF) for 4 days, with 3 replicates for each experiment; and a CloneSeq and a scRNAseq anlysis of ES cells grown with dox.

first: Danny

last: Bavli

first: Chen

last: Kozulin

first: Dena

last: Ennis

first: Alex

last: Motzik

first: Oren

last: Ram

first: Eran

last: Meshorer

first: Amnon

last: Buxboim


title: Testing in vitro tools for the prediction of cholestatic liver injury induced by non-pharmaceutical chemicals

status: Public on Mar 18 2021

city: Jette

first: Eva

middle: Anne D

last: Gijbels

state: Brussels

address: Laarbeeklaan 103, Building G, 2th floor, Department IVTD

country: Belgium

institute: VUB

summary: Bile acid accumulation and subsequent liver damage is a frequent adverse effect induced by drugs. Considerable efforts have therefore been focused on the introduction and characterization of tools that allow reliable prediction of this type of drug-induced liver injury. Among those are the cholestatic index and transcriptomic profiling, which are typically assessed in in vitro settings. The present study was set up to test the applicability of both tools to non-pharmaceutical compounds with cholestatic potential, including the industrial compound bis(2-ethylhexyl)phthalate, the cosmetic ingredients triclosan and octynoic acid, the herbicides paraquat and quizalofop-para-ethyl, and the food additives sunset yellow and tartrazine, in a human hepatoma cell culture model of cholestatic liver injury. The cholestatic index method showed cholestatic liability of sunset yellow, tartrazine and triclosan. Of those, tartrazine induced transcriptional changes reminiscent of the transcriptional profile of cholestatic drugs. Furthermore, a number of genes were found to be uniquely modulated by tartrazine, in accordance with the cholestatic drugs atazanavir, cyclosporin A and nefazodone, which may have potential as novel transcriptomic biomarkers of chemical-induced cholestatic liver injury. In conclusion, unambiguous identification of the non-pharmaceutical compounds tested in this study as inducers of cholestasis could not be achieved.

overall_design: HepaRG cells were exposed for 72 hours to 13 mM acetaminophen (APAP), 10 mM sunset yellow (SUN), 50 mM tartrazine (TART) and 0.050 mM triclosan (TRI)  in the presence of a 50 x concentrated bile acid mixture (BA). All in vitro experiments were conducted in 3 different HepaRG batches (CTL; BA; APAP + BA; SUN + BA; TART + BA; TRI + BA; n=3).

first: Lindsey

last: Devisscher

first: Mathieu

last: Vinken


title: ChIRC-seq  Reveals Promoter Antisense RNAs and HP1α as Key Regulators of Promoter Pause Release and of Enhancer : Architectural RNA Interactions [ChIP-Seq]

first: MICHAEL

last: ROSENFELD

first: Fan

last: Yang

first: Bogdan

last: Tanasa

first: Rudi

last: Micheletti

first: Kenneth

last: Ohgi

first: Michael

last: Rosenfeld


title: Transcriptomic profiling of Arabidopsis seedlings in response to mono-rhamnolipids from Pseudomonas aeruginosa secretome

status: Public on Mar 13 2021

city: Compiègne

first: Sonia

last: Rippa

address: Rue du Dr Schweitzer

department: Génie Biologique

institute: Université de Technologie de Compiègne

summary: Rhamnolipids (RLs) are known to trigger plant defense responses. In order to characterize the early and later gene expression of Arabidopsis thaliana after a mono-rhamnolipid treatment, ten-day-old Col-0 Arabidopsis seedlings were treated by root absorption with 100µM of mono-rhamnolipids (in 0.5% EtOH) or water (0.5% EtOH) and harvested after 1 or 3 hours. RNA samples were labelled, hybridized to Agilent Arabidopsis microarrays, washed, scanned and data acquired. Quality of the microarray data was checked.

overall_design: Gene expression in Arabidopsis seedlings was measured at 0, 1 and 3 hours after treatment with 100µM of purified mono-RLs (in 0.5% EtOH). Five biologically independent experiments were performed, including control samples with water (0.5 % EtOH), at each time.

first: Noadya

last: Monnier


title: Comparative transcriptome analysis of metastatic heterogeneity in a mouse model of breast cancer

city: Irvine

first: Ali

last: Mortazavi

state: California

address: 2218 Biological Sciences III

department: Developmental and cell biology

institute: University of California at Irvine

summary: We aimed to understand the transcriptome patterns of organ-derived cancer cell isolates from MMTV-PyMT mice. Tissues from primary tumors and organs harboring distal metastases were harvested from cancer bearing female mice. Although metastatic progression from primary tumors to lung tissue is well studied in the MMTV-PyMT model, metastases to other distal organs and the significance of intratumor heterogeneity across metastases from distal organs remain unclear.   To gain insight, we established an array of metastatic cell lines harvested from the MMTV-PyMT breast cancer mouse model. Sequencing at bulk and single-cell level were performed and used to examine the effects of cell heterogeneity on metastases and organ tropism

overall_design: For bulk RNA-seq we have 2 replicates per CD44 signature and tissue derived cell line, including mammary fat pad (MFP). For single-cell we have one rep per selected tissues.

first: Jennifer

last: Prescher

first: Anastasia

last: Ionkina

first: Gabriela

last: Balderrama


title: Defining genome architecture at base-pair resolution

status: Public on Apr 16 2021

city: Nanjing

first: Peng

last: Hua

state: Jiangsu

address: 101 Longmiandadao

department: State Key Laboratory of Reproductive Medicine and Offspring Health

institute: Nanjing Medical University

summary: By using a novel chromatin conformation capture (3C) method (Micro Capture-C (MCC)), which allows physical contacts to be determined at base-pair resolution. We demonstrate interactions between different classes of regulatory elements in unprecedented detail. T119_S12-S17 and E14_S10-S14 contains data of viewpoint from enhancers that are active in both ES and erythroid cells. NIPBL, CTCF and Rad21 CHIP libraries were prepared and analyzed as previously reported in Hanssen LLP. et al., 2017.

overall_design: MCC libraries were prepared from murine primary erythroid cells, embryonic stem cells or HUDEP-2 cells.


title: Simultaneous trimodal single cell measurement of transcripts, epitopes, and chromatin accessibility using TEA-seq

city: Seattle

first: Allen Institute

last: For Immunology

state: Washington

address: 615 Westlake Ave N, Seattle, WA

institute: Allen Institute

summary: Single-cell measurements of cellular characteristics have been instrumental in understanding the heterogeneous pathways that drive differentiation, cellular responses to signals, and human disease. Recent advances have allowed paired capture of protein abundance and transcriptomic state, but a lack of epigenetic information in these assays has left a missing link to gene regulation. Using the heterogeneous mixture of cells in human peripheral blood as a test case, we developed a novel scATAC-seq workflow that increases signal-to-noise and allows paired measurement of cell surface markers and chromatin accessibility: Integrated Cellular Indexing of Chromatin Landscape and Epitopes (ICICLE-seq). We extended this approach using a droplet-based multiomics platform to develop a trimodal assay that simultaneously measures Transcriptomics (scRNA-seq), Epitopes, and chromatin Accessibility (scATAC-seq) from thousands of single cells, which we term TEA-seq. Together, these multimodal single-cell assays provide a novel toolkit to identify type-specific gene regulation and expression grounded in phenotypically defined cell types.

overall_design:
PBMCs were profiled using a variety of multi-modal sequencing assays. We processed PBMCs through a number of single-cell and single-nuclei ATAC-seq protocols during development and identification of an optimized scATAC-seq assay. We processed PBMCs through our ICICLE-seq assay: a novel method for simultaneous profiling of chromatin accessibility and surface epitopes. We processed PBMCs through TEA-seq: a novel method for simulaneous single-cell profling of transcripts, epitopes, and chromatin accessiblity. As part of TEA-seq testing we prepared CITE-seq, scATAC-seq, single-cell and single-nuclei 10x Multiome ATAC + Gene Expression, and TEA-seq libraries from the same PBMC sample in parallel.

**The submitter declares that the raw data are being deposited in dbGaP due to patient privacy concerns. dbGap: phs002316**

first: Elliott

last: Swanson

first: Cara

last: Lord

first: Richard

last: Green

first: Thomas

middle: F

last: Bumol

first: Lucas

last: Graybuck

first: Peter

last: Skene


title: Gene expression analysis on the immortalized human mesothelial cell lines with different morphologies.

status: Public on Mar 31 2021

city: Aichi

first: Maho

last: Okuda

address: 1-1 Kanokoden, Chikusa-ku, Nagoya

department: Division of Cancer Biology

institute: Aichi Cancer Center Research Institute

summary: Establishment of immortalized human omental mesothelial cell lines (HOMCs) resulted in cloning three sublines (HOMC-B1, A4 and D4) with different morphologies. HOMC-B1 forms an epithelial-like monolayer. HOMC-A4 shows spindle-shaped morphology (storiform pattern). HOMC-D4 displayed an intermediate appearance. With the aim of exploring the key genes on decision of cellular morphology, gene expression of HOMC cell lines were analyzed along with conventional normal pleura-derived cell line, MeT-5A.

overall_design: Array analysis was performed with three HOMC cell lines with different morphology and human normal pleura transformant MeT-5A as reference cells.

first: Tatsuhiro

last: Sato

first: Yoshitaka

last: Sekido


title: Single-cell sequencing of peripheral blood mononuclear cells in acute Kawasaki disease

status: Public on Mar 12 2021

city: Shanghai

first: Zhen

last: Wang

address: 320 Yueyang Road

institute: Shanghai Institute of Nutrition and Health

summary: Kawasaki disease (KD) is the most common cause of acquired heart disease in children in developed countries. Based on single-cell RNA sequencing (scRNA-seq), we profiled peripheral blood mononuclear cells (PBMCs) from patients with acute KD before and after intravenous immunoglobulin (IVIG) therapy and from healthy controls. We identified the dynamics of cell abundance, gene expression patterns and biological processes underlying the immune dysregulation of each cell compartment. The single-cell landscape of both innate and adaptive immune responses provides new insights into pathogenesis and therapy of KD.

overall_design:
PBMCs from KDs before and after IVIG therapy, and healthy controls were subjected to scRNA-seq, scBCR-seq and scTCR-seq with 10x Genomics.
------------------------------------------
Authors state the following:
Raw data are deposited in the National Omics Data Encyclopedia (NODE) database (http://www.biosino.org/node/project/detail/OEP001162). Restrictions apply to the availability of these data, which are used under license for the current study and are not publicly available. Data are however available from the authors upon reasonable request and with permission of the NODE committee.

first: Lijian

last: Xie

first: Guohui

last: Ding

first: Yixue

last: Li

first: Min

last: Huang


title: Single-cell RNA Sequencing of Endometrial Assembloid Cultures

status: Public on Mar 08 2021

city: Coventry

first: Jan

last: Brosens

address: University Hospital Coventry and Warwickshire

department: Warwick Medical School

country: United Kingdom

institute: University of Warwick

summary: Decidual remodelling of midluteal endometrium leads to a short implantation window after which the uterine mucosa either breaks down or is transformed into a robust matrix that accommodates the placenta throughout pregnancy. To gain insights into the underlying mechanisms, we established and characterised endometrial assembloids, consisting of gland organoids and primary stromal cells. Single-cell transcriptomics revealed that decidualized assembloids closely resemble midluteal endometrium, harbouring differentiated and senescent subpopulations in both glands and stroma. We show that acute senescence in glandular epithelium drives secretion of multiple canonical implantation factors, whereas in the stroma it calibrates the emergence of anti-inflammatory decidual cells and pro-inflammatory senescent decidual cells. Pharmacological inhibition of stress responses in pre-decidual cells accelerated decidualization by inhibiting senescence and mesenchymal-epithelial transition, processes involved in endometrial breakdown and regeneration, respectively. Accelerated decidualization resulted in entrapment of co-cultured human blastocysts in a largely static decidual matrix. By contrast, the presence of senescent decidual cells created a dynamic implantation environment, enabling embryo expansion and attachment, although their persistence led to gradual disintegration of assembloids. Together, our findings demonstrate that senescence controls endometrial fate decisions at implantation and highlight how endometrial assembloids may accelerate the discovery of new treatments to prevent reproductive failure.

overall_design: Endometrial assembloids were prepared from cultured endometrial stromal cells and epithelial gland organoids. Assembloid cultures were grown for four days in Expansion Medium (ExM)+E2 , then either harvested (Day 0) or differentiated in the presence of 8-bromo-cAMP (cAMP), medroxyprogesterone acetate (MPA) and estradiol (E2) with or without the senolytic drug, dasatinib. Cells were recovered and subjected to single-cell analysis using nanoliter droplet barcoding and high-throughput sequencing of RNA (Drop-Seq).

first: Emma

middle: S

last: Lucas

last: Rawlings


title: mter-4 C. elegans RNA-seq

city: cambridge

first: Jonathan

middle: Lewis

last: Price

address: The Sanger Building Tennis Court Road

department: Biochemistry

institute: University of Cambridge

summary: Comparison of young adult wild-type and mter-4 mutants in C. elegans

overall_design: Young adult wild-type and mter-4 mutants were collected and frozen in Trizol. Samples were then sent to BGI for RNA extraction and DNBSeq PE100

first: Nick

last: Burton

first: Eric

last: Miska


title: Epigenomic Activation of Enhancers in Granule Cell Precursors by CHARGE Syndrome Protein CHD7 Regulates Gyrification of the Mammalian Cerebellum

status: Public on Apr 07 2021

city: st. louis

first: Naveen

last: Reddy

state: MO

address: 660 S Euclid Ave

institute: Washington University In St. Louis

summary: Regulation of chromatin plays fundamental roles in the normal development of the brain. Haploinsufficiency of the chromatin remodeling enzyme CHD7 causes CHARGE syndrome, a genetic disorder that prominently affects the development of the cerebellum. However, how CHD7 controls chromatin states in the cerebellum remains incompletely understood. Using conditional knockout of CHD7 in granule cell precursors in the mouse cerebellum, we find that CHD7 robustly promotes the accessibility and activity of enhancers in granule cell precursors. Remarkably, in vivo profiling of genome architecture reveals that CHD7 operates locally to stimulate enhancer activation, thereby driving the expression of topologically-interacting genes. Genome and gene ontology studies show that CHD7-regulated enhancers are associated prominently with genes that control brain tissue morphogenesis. Accordingly, conditional knockout of CHD7 triggers a striking phenotype of cerebellar polymicrogyria, which we have also found in a case of CHARGE syndrome. Finally, we uncover a CHD7-dependent switch in the preferred orientation of granule cell precursor division in the developing cerebellum, providing a cellular basis for the cerebellar polymicrogyria phenotype upon loss of CHD7. Collectively, our findings define CHD7 function in the regulation of the epigenome in granule cell precursors and identify a surprising link of CHD7 to the control of cerebellar cortical morphogenesis, with potential implications for our understanding of CHARGE syndrome.

overall_design: Examination of the role of CHD7 to regulate the epigenome and cerebellar folding in control and conditional knockout mice.

first: Shahriyar

middle: P

last: Majidi

first: Lingchun

last: Kong

first: Mati

last: Nemera

first: Cole

last: Ferguson

first: Michael

last: Moore

first: Tassia

last: Goncalves

first: Hai-Kun

last: Liu

first: James

last: Fitzpatrick

first: Guoyan

last: Zhao

first: Tomoko

last: Yamada

first: Azad

last: Bonni

first: Harrison

middle: W

last: Gabel


title: A natural antisense transcript of notch-1 regulates cell cycle

status: Public on Mar 03 2021

city: Sydney

first: Ramin

last: M Farahani

state: NSW

address: Westmead Hospital, Darcy Road

department: molecular biomedicine

institute: University of Sydney

summary: Here we demonstrate a natural antisense transcript of notch-1 that interacts with the sense transcript and regulates its availability and pace of G1 phase of cell cycle.

overall_design: mRNA profiles of Control, RNAi-antisense notch-1, and RNAi-sense notch-1 neural progenitor cells, Biological replicates: 1/group

middle: M

last: Farahani


title: De novo DNA methylation controls neuronal maturation during adult hippocampal neurogenesis [Dnmt_inVivo_RRBS]

status: Public on Mar 02 2021

city: Dresden

first: Gerd

last: Kempermann

state: Saxony

address: Tatzberg 41

institute: German Center for Neurodegenerative Diseases (DZNE)

summary: Dynamic DNA methylation controls gene-regulatory networks underlying cell fate specification. How DNA methylation patterns change during adult hippocampal neurogenesis and their relevance for the generation of new neurons from adult neural stem cells has, however, remained unknown. Here, we show that neurogenesis-associated de novo DNA methylation is critical for maturation and functional integration of adult-born hippocampal neurons. Cell stage-specific bisulfite sequencing revealed a pronounced gain of DNA methylation at neuronal enhancers, gene bodies and binding sites of pro-neuronal transcription factors during adult neurogenesis, which mostly correlated with transcriptional up-regulation of the associated loci. Inducible deletion of both de novo DNA methyltransferases Dnmt3a and Dnmt3b in adult neural stem cells specifically impaired dendritic outgrowth and synaptogenesis of new neurons, resulting in impaired hippocampal excitability and specific deficits in hippocampus-dependent learning and memory. Our results highlight that, during adult neurogenesis, remodeling of neuronal methylomes is fundamental for proper hippocampal function.

overall_design: Cell populations were isolated by FACS from the dentate gyrus of 11-week-old mice housed in standard conditions or in an enriched environment for five weeks

first: Sara

last: Zocher


title: Shape of promoter antisense RNAs regulates ligand-induced transcription activation

first: MICHAEL

last: ROSENFELD

summary: This SuperSeries is composed of the SubSeries listed below.

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: Refer to individual Series


title: De novo DNA methylation controls neuronal maturation during adult hippocampal neurogenesis [Dnmt_inVitro_RRBS]

overall_design: Neural precursor cell (NPC) cultures were generated from micro-dissected dentate gyrus tissue of nestin::CreERT2(-/-)-Dnmt3a-2lox-Dnmt3b-2lox one week after tamoxifen administration. NPC cultures were genotyped at Dnmt3a and Dnmt3b alleles and wildtype (WT) and double knock-out cultures (KO) were expanded and differentiated for five days to generate neurons. DNA methylation profiling was performed by RRBS on WT and KO NPCs and FAC-sorted neurons.


title: Mapping and modeling the genomic basis of differential RNA isoform expression at single-cell resolution with LR-Split-seq

first: Elisabeth

last: Rebboah

address: 2300E Biological Sciences 3

department: Developmental and Cell Biology

institute: University of California, Irvine

summary: The rise in throughput and quality of long-read sequencing should allow unambiguous identification of full-length transcript isoforms. However, its application to single-cell RNA-seq has been limited by throughput and expense. Here we develop and characterize long-read Split-seq (LR-Split-seq), which uses combinatorial barcoding to sequence single cells with long reads. Applied to the C2C12 myogenic system, LR-split-seq associates isoforms to cell types with relative economy and design flexibility. We find widespread evidence of changing isoform expression during differentiation including alternative transcription start sites (TSS) and/or alternative internal exon usage. LR-Split-seq provides an affordable method for identifying cluster-specific isoforms in single cells.

overall_design: Profiling of C2C12 myoblasts and differentiated C2C12 by short and long-read single-cell RNA-seq as well as single-cell ATAC-seq.

first: Fairlie

last: Reese

first: S

last: Mortazavi


title: De novo DNA methylation controls neuronal maturation during adult hippocampal neurogenesis [scRNA-seq]

overall_design: Hippocampal neural precursor cells were traced by injecting lentiviruses carrying a Cre-dependent Gfp vector into the dentate gyrus of nestin::Cre-ERT2(+/-)/Dnmt3a(fl/fl)-Dnmt3b(fl/fl) (KO) and nestin::Cre-ERT2(+/-)/Dnmt3a(wt/wt)-Dnmt3b(wt/wt) (WT) mice. Expression of Gfp and deletion of Dnmt3a/Dnmt3b were induced by administration of tamoxifen. Gfp-positive cells were isolated from the dentate gyrus of WT and KO mice by FACS after a chase period of four weeks (n = 4 mice per group).

first: Rupert

last: Overall


title: Nascent RNA sequencing defines dynamic aryl hydrocarbon receptor signaling responses to wood smoke particles

status: Public on Feb 24 2021

city: Denver

first: Arnav

last: Gupta

state: CO

address: 1400 Jackson St. K720

department: Pulmonary and Critical Care

institute: National Jewish Health


title: Comparison of WT vs. MHCII KO CD8 T cell transcriptomes from lungs of Mycobacterium tuberculosis infected mice

status: Public on Feb 25 2021

city: Worcester

first: Samuel

last: Behar

state: MA

address: 368 Plantation street, AS8-2006

institute: University of Massachusetts Medical School

summary: CD4 T cells are essential for immunity to tuberculosis because they produce cytokines including interferon-γ. Whether CD4 T cells act as “helper” cells to promote optimal CD8 T cell responses during Mycobacterium tuberculosis (Mtb) is unknown. We compared transcriptomes of purified lung CD8 T cells from Mtb infected WT and MHCII KO mice. Using two independent models, we validated RNA-seq results and showed that CD4 T cell help enhanced CD8 effector functions and prevented CD8 T cell exhaustion. We demonstrated synergy between CD4 and CD8 T cells in promoting the survival of infected mice. Purified helped, but not helpless, CD8 T cells efficiently restricted intracellular bacterial growth in vitro. Thus, CD4 T cell help plays an essential role in generating protective CD8 T cell responses against M. tuberculosis infection in vitro and in vivo. We infer vaccines that elicit both CD4 and CD8 T cells are more likely to be successful than vaccines that elicit only CD4 or CD8 T cells.

overall_design: CD8 T cells were purified using anti-CD8 beads from lungs of aerosolized Mtb (strain Erdman) infected WT or MHCII KO mice at 8 weeks post infection. Around 70 Mtb/lung were detected 1 day after infection.  Transcriptomes of purified CD8 T cells were analyzed. Replicates were CD8 T cells from indivisual WT or MHCII KO mice.

first: Yu-Jung

last: Lu


title: DNA methylation regulates haematopoietic development

status: Public on Feb 23 2021

city: Beijing

first: Di

last: Liu

address: No. 45 West Street, Beijing

institute: Xuanwu Hospital, Capital Medical University

summary: Focus on EHT and definitive hematopoiesis process including E10.0, E11.0, E14, Adult

overall_design: Examination of the whole genome DNA methylation modification using WGBS

first: Jie

last: Zhou


title: Nascent RNA sequencing defines dynamic aryl hydrocarbon receptor signaling responses to wood smoke particles [ATAC-seq]

summary: Transcriptional responses to wildfire smoke, an increasingly important cause of human morbidity, are poorly understood. Here, using a combination of precision nuclear run-on sequencing (PRO-seq) and the assay for transposase-accessible chromatin using sequencing (ATAC-seq), we identify rapid and dynamic changes in transcription and chromatin structure in Beas-2B airway epithelial cells after exposure to wood smoke particles (WSP). By comparing 30 and 120 minutes of WSP exposure, we defined three distinct temporal patterns of transcriptional induction and chromatin responses to WSP. Whereas transcription of canonical targets of the aryl hydrocarbon receptor (AHR), such as CYP1A1 and AHRR, was robustly increased after 30 minutes of WSP exposure, transcription of these genes and associated enhancers returned to near baseline at 120 minutes. ChIP-qPCR assays and AHR knockdown confirmed a role for AHR in regulating these transcriptional responses, and we applied bioinformatics approaches to identify novel AHR-regulated pathways and targets including the DNA methyltransferase, DNMT3L, and its interacting factor, SPOCD1. Our analysis also defined a role for NFkB as a primary transcriptional effector of WSP-induced changes in gene expression. The kinetics of AHR- and NFkB-regulated responses to WSP were distinguishable based on the timing of both transcriptional responses and chromatin remodeling, with induction of several cytokines implicated in maintaining the NFkB response. In aggregate, our data establish a direct and primary role for AHR in mediating airway epithelial responses to WSP and identify crosstalk between AHR and NFkB signaling in controlling pro-inflammatory gene expression.

overall_design: The Omni method for the Assay for transposase-accessible chromatin by sequencing (Omni-ATAC-seq) was performed in BEAS-2B airway epithelial cells exposed to WSP at 1 mg/ml for 30 and 120 min. All samples were sequenced in duplicate.

first: Sarah

last: Sasse

first: Margaret

last: Gruca

first: Lynn

last: Sanford

first: Robin

middle: D

last: Dowell

first: Anthony

middle: N

last: Gerber


title: Transcriptomics analysis of Komagataeibacter europaeus CGMCC 20445 during acetic acid fermentation

status: Public on Mar 09 2021

first: Huiming

last: Guo

address: NO.30 Puzhu Road

institute: Nanjing Tech University

summary: We conducted transcriptome analysis of Komagataeibacter europaeus CGMCC 20445 samples under different acidity conditions to elucidate the changes in differentially expressed genes throughout the fermentation process.

overall_design: Samples used for transcriptome sequencing were named as A10h (acidity: 1.38 g/100 mL), B10h (acidity: 1.44 g/100 mL), C10h (acidity: 1.46 g/100 mL), A40h (acidity: 2.22 g/100 mL), B40h (acidity: 2.40 g/100 mL), C40h (acidity: 2.40 g/100 mL), A64h (acidity: 3.06 g/100 mL), B64h (acidity: 3.30 g/100 mL), C64h (acidity: 3.18 g/100 mL), A88h (acidity: 3.96 g/100 mL), B88h (acidity: 4.32 g/100 mL), C88h (acidity: 3.96 g/100 mL).

first: Liting

last: Wang

first: Housheng

last: Hong


title: Overarching control of autophagy and DNA damage response by CHD6 revealed by modeling a rare human pathology [ATAC-Seq]

status: Public on Feb 22 2021

city: Goettingen

first: Argyris

last: Papantonis

address: Robert-Koch-Str 40

department: Department of Pathology

institute: University Medical Center Goettingen

summary: Members of the chromodomain-helicase-DNA binding (CHD) protein family are chromatin remodelers critically implicated in human pathologies, with CHD6 being one of its least studied members. Here, we discovered a de novo CHD6 missense mutation in a patient clinically presenting the rare Hallermann-Streiff syndrome (HSS). We used genome editing to generate isogenic iPSC lines and model HSS in relevant cell types. We show that CHD6 binds a cohort of autophagy and stress response genes across cell types. The HSS-mutation affects CHD6 protein folding and impairs its ability to recruit co-factors in response to DNA damage or autophagy stimulation. This leads to an accumulation of DNA damage burden and to senescence-like phenotypes. By combining genomics and functional assays, we describe for the first time a molecular mechanism for the chromatin control of autophagic flux and genotoxic stress surveillance that applies broadly to human cell types and explains HSS onset.

overall_design: Assay for Transposase-Accessible Chromatin using sequencing in iPS cells

first: Nadine

last: Übelmesser

first: Natasa

last: Josipovic

first: Tabea

last: Hugo


title: Nascent RNA sequencing defines dynamic aryl hydrocarbon receptor signaling responses to wood smoke particles [PRO-seq]

first: Arnav

last: Gupta

overall_design: Deep sequencing of nascent transcripts was performed using Precision Run-on sequencing (PRO-seq) in BEAS-2B cells airway epithelial cells following exposure to WSP. All samples were sequenced in duplicate.

middle: A


title: Accelerated passage of gene-modified monkeys by hormone-induced precocious puberty

first: Zhen

state: Shanghai

address: 320 Yue-Yang Rd

department: Center for Excellence in Brain Science and Intelligence Technology (CEBSIT)

institute: Institute of Neuroscience (ION), Chinese Academy of Sciences

summary: To evaluate the epigenetic status in sperm from the precocious monkeys, whole genome and single-base resolution maps of 5- methylcytosine (mC) analysis was performed by bisulfite-sequencing (BS-Seq) at an average depth of 15.4-fold per strand in DNA sample from the sperm of a naturally-matured monkey (#2) and 13.6-fold from a sexual precocious monkey (#49). Around 70% of all cytosine in genome were covered at least five times in each sample. We analyzed the average methylation levels and density of cytosinein two samples and found that there was no significant difference between the hormone-treated group and control group.

overall_design: Whole Genome Bisulfite Sequence (WGBS): naturally-matured monkey (#2) and  sexual precocious monkey (#49)

first: Qiang

last: Sun


title: YAP and TAZ are transcriptional co-activators of AP-1 proteins and STAT3 during breast cellular transformation (RNA-seq)

status: Public on Feb 18 2021

city: Boston

first: Kevin

last: Struhl

address: 240 Longwood Ave.

department: Biological Chemistry and Molecular Pharamcology

institute: Harvard Medical School

summary: The YAP and TAZ paralogues, the ultimate effectors of the Hippo signaling pathway, are  deregulated in many cancer types. They are transcriptional co-activators that are  recruited to their target sites, primarily by TEAD proteins. Here, we show that YAP and  TAZ are also recruited by JUNB and STAT3, key factors that mediate an epigenetic  switch linking inflammation to breast cellular transformation. YAP and TAZ directly  interact with JUNB and STAT3 via a WW domain that is important for transformation,  co-occupy many target sites in vivo via the sequence motifs of AP-1 and (to a lesser extent) STAT3, and stimulate transcriptional activation by AP-1 proteins. A small minority of  target sites are YAP- or TAZ-specific, and they are associated with different sequence  motifs and gene classes. YAP/TAZ, JUNB, and STAT3 directly regulate a common set  of target genes that overlap, but are distinct from, those regulated by YAP/TAZ and  TEADs. The set of target genes regulated by YAP/TAZ, STAT3, and JUNB is associated  with poor survival in breast cancer patients with the triple-negative form of the disease.

overall_design: YAP/TAZ, AP-1 and STAT3 transcriptional regulation in breast cancer

first: Zhiping

last: Weng

first: Lizhi

last: He

first: Henry

last: Pratt

first: Fengxiang

last: Wei

first: Mingshi

last: Gao


title: Epigenomic Landscape of Mouse Brain by Single Nucleus Methylation Sequencing [CEMBA190108_6A]

status: Public on Feb 19 2021

city: La Jolla

first: Joseph

middle: R

last: Ecker

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

summary: Illustrating the cellular architecture of the mammalian brain is critical to understanding its diverse functions and complex animal behaviors. With support from NIMH and NINDS as part of the BRAIN Initiative Cell Census Network (BICCN), the Center for Epigenomics of the Mouse Brain Atlas (CEMBA) applied single nucleus methylation sequencing in 118 brain funtional regions across the whole adult male P56 C57BL/6J mouse brain. In each major brain regions, we identified distinct cell clusters and formed them in a hierarchical taxonomy. These clusters include known primary brain cell types and possible sub-types. We use these data to identify the epigenomic characteristics and to define specific regulatory elements for each cell cluster. We integrate the single cell methylome with single cell gene expression and chromatin accessibility profiles from the same brain region to further identify potential enhancers and their corresponding genes for several neuronal cell types. By brain region spacial comparisons, we found spatial specificity among excitatory neuronal clusters within the same cortical layer. We identify brain-region-specific transcription factors that may regulate cortical region development of excitatory neurons. These data define the landscape of cell type and spatial heterogeneity in the mouse brain and the underlining regulatory epigenomic basis.

overall_design: Apply snmC-seq2 to 118 brain functional regions to identify epigenomic landcape of the adult mouse brain, this subseries consists of one single nucleus methylation sequencing experiment of brain region (ACA,PL,ILA).

first: Hanqing

last: Liu

first: Chongyuan

last: Luo

first: Angeline

last: Rivkin

first: Anna

last: Bartlett

first: Jacinta

last: Lucero

last: Nery

first: Andrew

last: Aldridge

first: Rosa

last: Castanon

first: Yupeng

first: Huaming

last: Chen

first: Zhuzhu

last: Zhang

first: Jingtian

last: Zhou

first: Bing

last: Ren

first: Eran

last: Mukamel

first: M

last: Behrens


title: Effect of CBL0137 on DIPG cells

status: Public on Mar 07 2021

first: Chi Nam Ignatius

last: Pang

address: School of Biotechnology and Biomolecular Sciences, UNSW Australia

department: The NSW Systems Biology Initiative

institute: The University of New South Wales

summary: Diffuse intrinsic pontine glioma (DIPG) is an aggressive and incurable childhood brain tumor for which new treatments are needed. A high throughput drug screen of 3600 pharmaceutical compounds found that anti-malarials, including quinacrine had potent activity against DIPG neurospheres. CBL0137 is a novel anti-cancer compound developed from quinacrine, which targets Facilitates Chromatin Transcription (FACT), a chromatin remodelling complex involved in transcription, replication, and DNA repair. We have found that CBL0137 displays profound cytotoxic activity against a panel of patient derived DIPG cultures, inhibiting cell proliferation and clonogenic potential, restoring tumor suppressor TP53 and Rb activity and inducing cell death through induction of apoptosis. Moreover, in an orthotopic model of DIPG, treatment with CBL0137 significantly extended animal survival. Histone mutations leading to the loss of histone trimethylation result in epigenetic dysregulation driving DIPG tumorigenesis. Treatment with CBL0137 targets this epigenetic defect, restoring both histone H3.3 acetylation and trimethylation and leading to tumor cell death. Combined epigenetic treatment with the histone deacetylase (HDAC) inhibitor panobinostat led to inhibition of the Rb/E2F1 pathway, and increased the enzymatic activity of enhancer of zeste homolog 2 (EZH2), leading to the restoration of H3K27 trimethylation. This combination therapy had synergistic activity against DIPG neurospheres with induction of apoptosis. Consistent with the in vitro results, the combination of CBL0137 and panobinostat significantly prolonged the survival of mice bearing DIPG orthografts suggesting a potential treatment strategy for DIPG.

overall_design: HSJD-DIPG007 cells were treated with DMSO, CBL0137 (0.6?M), panobinostat (20nM) and the combination of the two agents for 24 hours. After incubation, cells were harvested and washed 2x with PBS. RNA was then extracted using the RNeasy extraction kit (Qiagen) according to the manufacturer’s instruction. Gene expression data was obtained through the Affymetrix Clariom D Human microarray platform, containing 6,281,169 probes and 40,899 probesets. Probesets were processed using the Robust MultiArray (RMA) pipeline (PMID 21070630) followed by probeset annotation to gene symbols using the Bioconductor AnnotationDbi pipeline (PMID 16939789).

first: Anhaid

last: Ehteda

first: Sandy

last: Simon

first: Laura

last: Franshaw

first: Federico

last: Giorgi

first: Jie

first: Elisha

last: Hayden

first: Swapna

last: Joshi

first: Chi

first: Ruby

last: Pandher

first: Chelsea

last: Mayoh

first: Aaminah

last: Khan

first: Caitlin

last: Ung

first: Ornella

last: Tolhurst

first: Anne

last: Kankean

first: Anjana

last: Gopalakrishnan

first: Peter

last: Trebilcock

first: Katerina

last: Gurova

first: Andrei

last: Gudkov

first: Murray

last: Norris

first: Michelle

last: Haber

first: Orazio

last: Vittorio

first: Maria

last: Tsoli

first: David

last: Ziegler


title: The small RNA SprY controls RNAIII function and affects Staphylococcus aureus virulence

status: Public on Feb 10 2021

city: Rennes

first: Vincent

last: Cattoir

address: 2 rue Henri Le Guilloux

institute: CHU de Rennes

summary: While a plethora of small regulatory RNAs (sRNAs) have been identified in the human pathogen Staphylococcus aureus, the physiological function of most of them remains unknown. We report the characterization of SprY, a sRNA from S. aureus expressed from a pathogenicity island. RNAIII, a major regulator of S. aureus virulence, was discovered as a potential SprY target by an MS2-affinity purification assay. In silico interaction studies suggest a RNA-RNA pairing between the SprY 5’end and the 13rd stem-loop of RNAIII. Overproduction of SprY leads to a 1.5-fold reduction of RNAIII amount. By affecting the rnaIII expression, SprY affects the amount of RNAIII known targets. Indeed, SprY downregulates hla mRNA translation, but also upregulates other secreted factors such as Ecb and Rot. Furthermore, SprY decreases the hemolytic activity and virulence of S. aureus. Our results lead to propose that SprY is involved in S. aureus virulence through a post-transcriptional regulation of RNAIII.

overall_design: Transcriptome analysis by RNA-seq to monitor the levels of all transcripts in bacterial cells grown in the absence or the presence of a subinhibitory concentration (8 mg/L) of caspofungin.

first: Kim

middle: B

last: Le Huyen

first: Cintia

last: Gonzalez

first: Gaetan

last: Pascreau

first: Valérie

last: Bordeau

first: Wenfeng

last: Liu

first: Philippe

last: Bouloc

first: Brice

last: Felden

first: Svetlana

last: Chabelskaya


title: SNHG17 Interacts with LRPPRC to Stabilize c-Myc and Promote G1/S Transition and Cell Proliferation

city: Guangzhou

first: shimei

last: zhuang

state: Guangdong

address: Xin Gang Xi Road 135#

department: School of Life Sciences

institute: Sun Yat-sen University

summary: Long non-coding RNAs (lncRNAs) emerge as new regulators of various cell activities. The G1 to S phase (G1/S) transition is the key step that drives cell to the division cycle, and its dysregulation contributes to unrestrained cell proliferation and consequent tumor development.In this study, we examined lncRNA expression profiles during cell cycle using serum starvation-stimulation model in human skin fibroblasts (SFs) and identified that lncRNA SnoRNA Host Gene 17 (SNHG17) was elevated at the early G1 phase and in hepatocellular carcinoma (HCC) tissues. Both gain- and loss-of function studies disclosed that SNHG17 increased c-Myc protein level, accelerated G1/S transition and cell proliferation, and consequently promoted tumor growth. Up-regulation of SNHG17 was correlated with high c-Myc level in human HCC. Mechanistically, the 1-150-nt of SNHG17 physically interacted with the 1035-1369-aa of leucine rich pentatricopeptide repeat containing (LRPPRC) protein, and disrupting this interaction abrogated the promoting role of SNHG17 in c-Myc up-regulation, G1/S transition and cell proliferation. And the proliferation-stimulatory effect of SNHG17 was abrogated by silencing c-Myc or LRPPRC. Furthermore, silencing SNHG17 or LRPPRC increased the ubiquitylated c-Myc level and reduced c-Myc stability, suggesting that SNHG17 may inhibit c-Myc ubiquitination and thus enhance c-Myc level and facilitate proliferation by interacting with LRPPRC. Our findings identify a novel SNHG17-LRPPRC-c-Myc regulatory axis and elucidate its roles in G1/S transition and tumor growth, which provide potential targets for cancer therapy.

overall_design: Human primary  skin fibroblasts （SFs）were isolated from human neonatal foreskin  and cultured in RPMI 1604 medium supplemented with 10% FBS , 100 mg/mL streptomycin and 100 U/mL penicillin in a humidified atmosphere with 5% CO2 at 37 ℃. SFs were induced to enter a quiescent state by depriving serum for 48 hours and then stimulated to enter the G1 phase and subsequent S phase by adding serum. RNA Sequecing was performed  in biological duplicates for SFs at 0, 4, and 18 hours after serum re-addition.

first: Jin-Yu

first: Shi-Mei

last: Zhuang


title: Transcriptomic analysis of miR-204-3p-overexpressed human monocyte-derived macrophages (HMDMs)

status: Public on Feb 03 2021

first: Si-Jia

last: Liang

address: 74 Zhongshan 2 Rd

department: Pharmacology

institute: Zhongshan School of Medicine, Sun Yat-Sen University

summary: HMDMs were transfected with miRNA mimics negative control or miRNA-204-3p mimics for 24 hours, and then were sequenced to determine gene expression profiles.

overall_design: RNA-seq of HMDMs treated with miRNA mimics control or miR-204-3p mimics


title: CRISPR activation of endogenous genes reprograms fibroblasts into cardiovascular progenitor cells

status: Public on Feb 01 2021

city: Cincinnati

first: JIALIANG

last: LIANG

address: 231 Albert Sabin Way

department: Department of Pathology and Laboratory Medicine

institute: University of Cincinnati

summary: In this study, we determine whether direct activation of endogenous loci by targeting the genomic DNA (using a CRISPRa system) can fulfill reprogramming of fibroblasts into cardiac progenitors. Core promoter regions of Gata4, Nkx2-5, and Tbx5 were targeted by the CRISPRa (Synergistic Activation Mediator) in mouse tail tip fibroblasts (TTFs). RNA sequencing was performed to characterize the transcriptome of the transfected fibroblasts and reprogrammed cells. These data indicate that our CRISPRa approaches can induce cardiac reprogramming and establish a gene network for heart development.

overall_design: RNA-seq of fibroblasts, early reprogrammed cells, and CRISPR-induced cardiac progenitors (ciCPCs).

first: Jialiang

first: Lin

last: Jiang


title: Identification of sequence-specific promoters driving polycistronic transcription initiation by RNA Polymerase II in trypanosomes

city: Granada

first: Carlos

last: Cordon-Obras

address: Av del Conocimiento

country: Spain

institute: Instituto Parasitologia Lopez Neyra

summary: Protein coding genes in the trypanosome genome are organized in polycistronic transcription units (PTUs). How RNA Polymerase II (Pol II) initiates PTU transcription has not been resolved and the current model favors initiation driven by chromatin epigenetic marks, rather than core-promoters. Here, we identify sequence-specific core promoters by functional characterization of ChIP-Seq Pol II accumulation-peaks. Sequences located between oppositely orientated PTUs contained two independent and distinct core promoters, driving unidirectional transcription. Detailed analysis of one promoter identified 75 bp, necessary and sufficient to fully drive reporter expression, and containing short functional motifs. Analysis of further promoters suggested activity and initiation is regulated and both, focused and dispersed transcription patterns were found. Thus, in contrast to the model of unregulated and promoter-independent transcription initiation, sequence-specific promoters determine the initiation of RNA Pol II transcription of protein coding genes in trypanosomes. These findings resolve the discrepancy between trypanosomes and other eukaryotes in how Pol II initiates protein-coding gene transcription.

overall_design: ChIP-Seq analysis of RNA pol II accumulation in Trypanosoma brucei brucei using anti-RPB1 antibodies and sequenced in Illumina NextSeq 500.

first: Claudia

last: Gomez

first: Sara

last: Torres-Rusillo

first: Isabel

last: Vidal

first: Diana

last: Lopez-Farfan

first: Alicia

last: Barroso

first: Domingo

last: Rojas-Barros

first: Mark

last: Carrington

first: Miguel

last: Navarro


title: De novo DNA methylation controls neuronal maturation during adult hippocampal neurogenesis.

first: Gerd

last: Kempermann

overall_design: Refer to individual Series


title: Combination of CBL0137 and Panobinostat in DIPG

status: Public on Feb 12 2021

first: Chi Nam Ignatius

last: Pang

overall_design: HSJD-DIPG007 cells were treated with DMSO, CBL0137 (0.6μM), panobinostat (20nM) and the combination of the two agents for 24 hours. After incubation, cells were harvested and washed 2x with PBS. RNA was then extracted using the RNeasy extraction kit (Qiagen) according to the manufacturer’s instruction. Gene expression data was obtained through the Affymetrix Clariom D Human microarray platform, containing 6,281,169 probes and 40,899 probesets. Probesets were processed using the Robust MultiArray (RMA) pipeline (PMID 21070630) followed by probeset annotation to gene symbols using the Bioconductor AnnotationDbi pipeline (PMID 16939789).

first: Anhaid

last: Ehteda

first: Sandy

last: Simon

first: Laura

last: Franshaw

first: Federico

last: Giorgi

first: Jie

last: Liu

first: Elisha

last: Hayden

first: Swapna

last: Joshi

first: Chi

first: Ruby

last: Pandher

first: Chelsea

last: Mayoh

first: Aaminah

last: Khan

first: Caitlin

last: Ung

first: Ornella

last: Tolhurst

first: Anne

last: Kankean

first: Anjana

last: Gopalakrishnan

first: Peter

last: Trebilcock

first: Katerina

last: Gurova

first: Andrei

last: Gudkov

first: Murray

last: Norris

first: Michelle

last: Haber

first: Orazio

last: Vittorio

first: Maria

last: Tsoli

first: David

last: Ziegler


title: The Drosophila Brain on Cocaine at Single Cell Resolution

status: Public on Jan 29 2021

city: Greenwood

first: Vijay

last: Shankar

state: South Carolina

address: 115 Milford Pines Drive

institute: Clemson University

summary: To identify specific cell populations that respond to acute cocaine exposure, we analyzed single cell transcriptional responses in duplicate samples of flies that consumed fixed amounts of sucrose or sucrose supplemented with cocaine, in both sexes. Unsupervised clustering of the transcriptional profiles of a total of 86,224 cells yielded 36 distinct clusters. Annotation of clusters based on gene markers revealed that all major cell types (neuronal and glial) as well as neurotransmitter types from most brain regions were represented. The brain transcriptional responses to cocaine showed profound sexual dimorphism and were considerably more pronounced in males than females. Differential expression analysis within individual clusters indicated cluster-specific responses to cocaine. Clusters corresponding to glia and Kenyon cells of the mushroom bodies showed especially large transcriptional responses following cocaine exposure. Cluster specific co-expression networks and global interaction networks revealed a diverse array of cellular processes affected by acute cocaine exposure. These results provide an atlas of sexually dimorphic cocaine-modulated gene expression in a model brain.

overall_design: Profiling of 8 samples consisting of 20 Drosophila brains each, 2 conditions (sucrose and cocaine), 2 sexes (male and female) and 2 replicates

first: Brandon

last: Baker

first: Sneha

last: Mokashi

first: Jeffrey

last: Hatfield

first: Rachel

middle: C

last: Hannah

first: Trudy

last: Mackay

first: Robert

last: Anholt


title: 10X genomics single cell RNA sequencing of tumor sections from tumor bearing KrasG12D/+Lkb1fl/fl(KL) mice after Ad-cre injection for 10 weeks

status: Public on Jan 28 2021

city: Wuhan

first: 鹏

last: 王

email: wangp00678@163.com, wangp94@whu.edu.cn

state: 湖北省

address: 169 Donghu nan road,Wucang District

country: China

institute: 武汉大学

summary: Tumor-infiltrating cells comprise many celltypes, including monocytes, macrophages, dendritic cells, neutrophils, stromal cells and epithelial cells, and have emerged as key regulators of cancer growth. These cells can diversify into a spectrum of states, which may promote or limit tumor outgrowth, but remain poorly understood. Here, we used single-cell RNA sequencing to map cell heterogeneity in non-small cell lung cancer mouse model. We uncovered 11 cell types in tumor sections, most of which were reproducibly found across tumor bearing mice. we obtained a series of genes which expression levels were very low, such as cytokines and chemokines. It is very helpful for us to understand the signal cascade and ligands-receptors interaction between different cell types.

overall_design: Single cell RNA sequencing (scRNAseq) of RBC-depleted cells from tumor sections of  2 tumor-bearing KL mice.

first: P

last: Wang

first: B

last: Zhong


title: Single-cell ATAC-Seq of Adult GBM surgical specimens

status: Public on Jan 27 2021

city: Calgary

first: Marco

last: Gallo

state: Alberta

address: 3330 Hospital Drive NW, Heritage Medical Research Building

department: Cumming School of Medicine

institute: University of Calgary

summary: We performed scATAC-seq on primary glioblastoma tissue samples taken at time of initial resection to map the global chromatin profiles of glioblastoma cells and associated non-neoplastic cells

overall_design: scATAC-seq of primary patient-derived adult glioblastoma tissue

first: Divya

last: Singhal

first: Ana

last: Nikolic

first: Katrina

last: Ellestad


title: X-ray causes mRNA transcripts change to enhance Orai2-meadated Ca2+ influx in rat brain microvascular endothelial cells

status: Public on Feb 04 2021

city: Hefei

first: Lesha

last: Zhang

state: Anhui

address: 81 Meishan road

department: Physiology

institute: Anhui Medical University

summary: We utilized high-throughput sequencing and subsequent signaling pathway analyses to find all the 2 fold change expression of transcripts in comparison of brain microvascular endothelial cells derived from six Sprague Dawley rats without or with irradiation at the dose of 5 Gy or 20 Gy and then cultured for 12 h or 24 h

overall_design: The RNA sample libraries containing all the 150 base pairs of  rats‘ brain microvascular endothelial cells without or with irradiation at the dose of 5 Gy or 20 Gy and then cultured for 12 h or 24 h were established and sequenced using the high-throughput Illumina HiSeq 2500 sequencing platform, then mapped to the rat reference genome with HISAT2 (version 2.0.13) , converted to a binary BAM file through samtools (version 1.9) , and assembled into single complete transcripts through StringTie (version 1.3.5) software, following with GO and KEGG pathway enrichment analyses and gene expression pattern analysis.

first: Fangfang

last: Xu

first: Yang

first: Qibing

last: Wu


title: Transcriptomics Library Data of Klutuk Wulung Banana with Ethylene Treatment

status: Public on Jan 31 2021

city: Bandung

first: Fenny

last: Dwivany

address: Jl. Ganesha No. 10

country: Indonesia

institute: Institut Teknologi Bandung

summary: We report the first RNA sequencing data of 100μl/L ethylene treatment and non-treatment (control) fruit of Musa balbisiana (BB Group, Cv. Klutuk Wulung) at unripe (day 1) and ripe (day 7) stage

overall_design: Examination of fruit pulp mRNA of non-treatment (control) and ethylene treatment (100μl/L) fruit of Klutuk Wulung banana (Musa balbisiana, BB Group)

first: Husna

last: Nugrahapraja

first: Lutfi

last: Sari

first: Rika

last: Putri

first: Cindy

last: Novianti